They wrote to the Directorate of Film Festivals they were not "boycotting the awards" but felt "dejected rather than honoured for our work" because of how these were to be handed over.
They claimed the 65-year-old awards had always been presented by the President. Sometimes the President had stepped off the stage to hand an award over.
Thursday's event was divided into halves, Irani presenting 60-odd awards before Kovind arrived and handed over the 11 main prizes, including the Dadasaheb Phalke Award.
Before the start of the ceremony, Directorate of Film Festivals officials had removed the nameplates for 70 awardees, who had earlier in the day sent the letter indicating their intent to skip the event.
But 15 of them, including singer Yesudas and Malayalam director Jayaraj, both of whom were among the select 11, eventually did turn up.
To limit Irani's embarrassment, directorate officials refrained from announcing the names of the signatories who they were certain would not yield to last-minute persuasions despite chief jury Shekhar Kapur meeting them twice during the day as a government emissary.
Still, there were moments when an awardee's name was called out and Irani, along with her junior Rajyavardhan Singh Rathore, waited for the recipient to come forward in vain.
Ministry officials said their hands were tied as it was Rashtrapati Bhavan that had decided the President would not spend more than an hour at the event, which normally clocks at least two hours.
Some officials suggested the protest was driven by mischief-makers among the awardees. They said the awardees had been told clearly at Wednesday's rehearsal that the new protocol was the President's decision.
But the protesters asked why the invitations - and even Thursday's newspaper ads - did then state that the President would hand over the awards in the presence of the two ministers.
"It feels like a breach of trust when an institution/ceremony that abides by extreme protocol fails to inform us of such a vital aspect of the ceremony with a prior notice. It seems unfortunate that 65 years of tradition are being overturned in a jiffy," the letter said.
Rahul Dholakia, who won the award for his film Parzania in 2005, expressed solidarity with the protesters, tweeting: "One of the reasons the National Film Awards are prestigious is (that) they are handed by the @rashtrapatibhvn - not a minister.This is a moment of a lifetime for filmmakers; please don't deprive them of their merit/glory."